Ericoid Mycorrhizal fungi have been shown to form symbiotic associations with Erious plants and increase nutrients uptake by the plant. The objective of this study was to assess the potential of two ericoid mycorrhizal isolates Oidiodendron maius and Pezizella ericae as potential sources of inoculant for rabbiteye blueberry (Vaccinium ashei) and to assess the variation in consistency and degree of ericoid mycorrhizal fungi colonization within rabbiteye blueberry (Vaccinium ashei). Field trials were conducted in 2012 in Verona, MS at the North Mississippi Research and Extension Center. In this study data was collected on fruit yield, leaf tissue nutrient concentration, leaf tissue nitrogen concentration, and percent colonization of root tissue. Ericoid mycorrhizal fungal isolates Oidiodendron maius and Pezizella ericae showed no influence on rabbiteye blueberry (Vaccinium ashei) during this study.

Diversity of ectotrophic mycorrhizal (EM) fungi on out-planted seedlings of two oak species (Quercus rubra and Q. prinus) was estimated at two sites in mature mixed forests in the southern Appalachian mountains. Late – stage fungi were well represented. Total richness was 73 types, with 42 types having a frequency of only one. Thelephoroid / tomentelloid, russuloid, and cortinarioid groups were the richest. Dominant fungi included a putative Tuber sp. and Craterellus sp., and Laccaria cf laccata. Diversity was lower at a high elevation chestnut oak dominated site compared to a lower mesic cove – hardwood forest site. There was little evidence for fungal specificity to red oak versus white oak seedlings. We also compared EM fungus distributions on root systems of oak seedlings from samples taken in mid-July and early-September. The majority of EM types occurred only in the mid- or late-summer samples respectively. Dramatic shifts in mycobiont dominance were observed in relation to sample date, including increases in Cortinarius spp. richness, decreases in Thelephoraceae richness, and the disappearance of Amanita spp. types in the late- compared to mid-summer samples. A multi-stage model of seasonal EM dynamics is proposed, with implications for the niche expansion of associated phytobionts. In this model, generalistic mycobionts are most frequent and occur throughout the season. Other more specialized fungi show seasonal specificity. Relationships between species and communities of EM fungi and environmental parameters such as ericoid shrub abundance and edaphic characteristics were also examined. High diversity of EM fungi limited resolution of community level relationships given our sample sizes. Intraspecific variation in EM fungi with regard to microsite characteristics was also undetectable. No association between ericoid shrub dominance (Kalmia latifolia and Rhododendron maximum) and EM fungi was observed. We present a listing of EM fungus types with associated ranges of edaphic parameters and ericoid shrub abundance. The family Sebacinaceae is a basal hymenomycete lineage that includes members of the genera Tremellodendron and Sebacina. We present evidence suggesting the putative mycorrhizal status of two species of Tremellodendron. Tremellodendron appears to form both endophytic associations with achlorophyllous orchids and ectomycorrhizae with species of Quercus, Pinus and Tilia cordata. / Ph. D.

Two hundred and forty three fungal isolates were obtained from roots of four Woollsia pungens (Cav.) F. Muell plants collected from a field site in New South Wales, Australia. 175 sterile isolates were slow growing and dark-coloured on 2 percentage malt agar and were selected for further analysis. Microsatellite-primed PCR using the primers (GACA)4 and (GTG)5 separated these isolates into 50 genets. Isolates representative of 43 genets (including 168 isolates in total) formed typical ericoid mycorrhizal structures when inoculated onto roots of Vaccinium macrocarpon Ait (Ericaceae), confirming their status as mycorrhizal endophytes. It was estimated that a minimum of 43 genetically-distinct mycorrhizal mycelial genets were present in the root systems of the sampled W. pungens population with 7 to 15 distinct endophytic genets identified in each host plant, indicating that considerable genetic diversity exists within the endophyte population. While most genets were represented by less than 8 isolates, 3 genets contained up to 41 isolates, suggesting that root system colonisation by some mycelia may be extensive. While most fungal genets were shown to be confined to individual plants, 2 genets (genets 32 and 33), however, were present within the root systems of 2 adjacent plants (plants C and D), suggesting that the two root systems were interconnected by the endophyte mycelia. The ITS region of 13 mycorrhizal endophytes and a non-mycorrhizal isolate selected from the endophyte population were sequenced and compared to the sequence of Hymenoscyphus ericae as well as sequences from the GenBank database. A phylogenetic tree was generated from the nucleotide sequence data. This analysis revealed that 6 putative taxa were present in the root systems of 4 host plants. No isolates were positively identified to genus or species level. Closest matches with fungal sequences in the database indicated that most isolates probably belonged to the order Leotiales. Cluster analysis on the basis of the ITS sequences indicated that H. ericae was not clustered together with any endophytes from W. pungens, suggesting that endophytes of W. pungens are not identical to the known ericoid mycorrhizal fungus H. ericae. H. ericae had a low degree of sequence similarity with isolates from W. pungens, with similarities ranging from 68.3-80.6%. Cluster analysis based on DNA sequences of the ITS region did not fully support the groupings inferred from microsatellite-based fingerprinting. / Master of Science (Hons)

En raison des activités anthropiques croissantes, de larges sites sont contaminés par les métaux lourds qui affectent les systèmes biologiques. La souche Oidiodendron maius Zn pourrait être un organisme intéressant dans un programme de bioremédiation étant à la fois un champignon mycorhizien éricoïde et une souche tolérante aux métaux lourds. Pour comprendre les mécanismes de la tolérance de cette souche, trois approches différentes ont été menées.La première approche a abouti à la génération de mutants du gène superoxyde dismutase 1 (OmSOD1). Il s'agit de la première délétion d'un gène par recombinaison homologue chez un champignon mycorhizien. Nous démontrons que l'absence d'OmSOD1 cause un déséquilibre dans l'homéostasie rédox et un changement dans le dialogue entre le champignon et sa plante hôte.La deuxième approche a été basée sur la complémentation fonctionnelle d'un mutant de levure en utilisant une banque d'ADNc d'O. maius. Nous décrivons les premiers transporteurs d'un champignon mycorhizien éricoïde capables de conférer la tolérance au Zn dans des levures. Deux gènes ont été isolés et nommés OmCDF et OmFET. L'expression hétérologue de ces deux gènes dans différents mutants de levure a permis de conférer la tolérance au Zn. De plus, OmCDF a également permis de conférer la tolérance au Co. Nos données suggérent que OmCDF est un transporteur de Zn responsable du transfert du Zn cytoplasmique vers le réticulum endoplasmique, tandis que l'expression d'OmFET pourrait neutraliser la toxicité engendrée par le Zn en augmentant le contenu du Fe dans la cellule. La troisième approche a concerné le criblage d'une collection de mutants aléatoires d'O. maius sur Zn, Cd et ménadione. Nous décrivons la caractérisation d'un mutant dans le gène nmr. Dans ce mutant, une diminution de la teneur en glutamine et asparagine, ainsi qu'une réduction de l'activité de la glutamine synthétase ont été enregistrées. Les liens possibles entre la tolérance au stress oxydatif et le métabolisme azoté sont discutés. / Due to increasing anthropogenic activities, large areas are highly contaminated by heavy metals which are affecting biological systems. Oidiodendron maius strain Zn could be an interesting organism in a bioremediation program being both an ericoid mycorrhizal fungus and a heavy metal-tolerant strain. To understand the mechanisms underlying the oxidative stress tolerance of this strain, three different approaches were used. The first approach allowed us to obtain superoxide dismutase 1 (SOD1) null mutants. The most important technical advance in this work was the first successful disruption of a gene by homologous recombination in a mycorrhizal fungus. We demonstrate that the lack of OmSOD may cause an imbalance in the redox homeostasis and an alteration in the delicate dialogue between the fungus and its host plant. The second approach was based on a yeast functional complementation screening using an O. maius cDNA library. In this work we report the first transporters of an ericoid mycorrhizal fungus capable of conferring Zn tolerance to yeast transformants. Two full-length cDNAs were isolated and named OmCDF and OmFET. The heterologous expression of these two genes in various yeast mutants conferred resistance to zinc. Additionally, OmCDF expression also conferred Co tolerance. We provide evidence that OmCDF functions as a Zn transporter responsible for relocating cytoplasmic Zn into the endoplasmic reticulum, whereas expression of OmFET could counteract Zn toxicity by increasing Fe content of cells. The third approach consisted in the screening of a collection of O. maius random-mutants on Zn, Cd and menadione. We report the characterization of an O. maius-mutant that carries a mutation in the nmr gene. In this mutant, a decrease of glutamine and asparagine pools, and a reduction of the activity of glutamine synthase were recorded. Possible links between the oxidative stress tolerance and the nitrogen metabolism are discussed.

The origin and classification of open and mosaic ecosystems, particularly in the tropics and subtropics, have led to controversy worldwide. This has affected biodiversity conservation and, in some cases, promoted the establishment of afforestation projects based on the assumption that open and mosaic ecosystems are degraded forests. Although this initiative can have benefits in terms of carbon storage and climate mitigation if carefully planned and managed, it can also cause biodiversity loss and degradation when afforestation takes place in areas that were previously open ecosystems, or where unsuitable species are used. Madagascar, a world biodiversity hotspot, is one of the countries targeted for the implementation of afforestation projects. The Central Highlands of Madagascar, dominated by grassland matrix with forest patches, is the main region targeted. The nature and origin of the landscape are hotly debated, however, and it is not clear whether these open ecosystems are ancient or anthropogenically derived. Understanding of landscape history is therefore required to identify and conserve ancient open ecosystems, and to distinguish them from areas that have been deforested by people. This research aims to reconstruct the vegetation history and environmental change in the Central Highlands of Madagascar during the Holocene using palaeoecological methods, in order to inform appropriate conservation and management plans. We provide new records of vegetation, hydrological change, fire and herbivory activities by using a multiproxy approach, which includes fossil pollen, stable carbon isotopes, diatoms, charcoal and coprophilous spores, that allows for a comprehensive investigation into the history and drivers of vegetation change. Sediment cores were collected from two sites, Tampoketsa-Ankazobe wetland and Lake Dangovavy, located in the eastern and western slopes of the highlands, respectively. Results indicated that the surrounding area of both sites was composed of mosaic ecosystems, comprising of forest patches of variable extent in a matrix of open grassland and ericoid shrubland vegetation, at least from the Early and Mid-Holocene to ca. 1000 cal years BP, driven mainly by climate variability and fire occurrence. In Tampoketsa-Ankazobe wetland (eastern slopes), the vegetation was characterised by a mosaic of ericoid shrubland and mid-elevation forest taxa, between ca. 11 200 and 8300 cal years BP, under warm/wet period and low fire occurrence. The vegetation in the area changed to a mosaic of ericoid shrubland with more dominance of high-elevation forest from ca. 8300 to 1000 cal years BP under a drier climate and consistent low fire occurrence. The abundance of shrubs and trees during those two periods were confirmed by the dominance of C3 plants as reflected by the stable carbon isotopes results, and coincided with low herbivory activities in the TampoketsaAnkazobe site from ca. 11 200 to 1000 cal years BP. In parallel, the pollen record from Lake Dangovavy (western slopes), between ca. 6200 and 5400 cal years BP, suggests a mosaic ecosystem, dominated by more C3 montane grass, ericoid shrubland and high elevation forest patches promoted by cool/dry climate with low fire occurrence and herbivory activities. Between ca. 5400 and 4200 cal years BP, vegetation in the area was dominated by a mosaic of ericoid shrubland and mid-elevation forest under a wetter period, moderate fire occurrence, and herbivory activities. This mosaic was controlled by climate, fire refugia and herbivory feedbacks. The vegetation changed into a forest-savanna mosaic with an abundance of grassland and pioneer/fire-resistant trees between ca. 4200 and 3000 cal years BP. The period was characterised by an initial increase of local fire followed by a regional drought event. This suggests that a threshold might have been reached, with a resulting shift in vegetation composition. Between ca. 3000 and 1000 cal years BP, reoccurrence of ericoid shrubland with woodland savanna taxa was recorded in the area. The vegetation was conditioned by variation of climate from wet (until ca. 2000 cal years BP) to dry period (ca. 2000–⁠1000 cal years BP) with moderate fire occurrence and herbivory activities. In addition, stable carbon isotope results show that between ca. 6200 to 1000 cal years BP, the site was characterised by C3 plants. During the last ca.1000 cal years BP, pollen records from both sites in the Central Highlands of Madagascar showed a shift to a more open landscape dominated by grassland. Trees and shrubland in the highlands experienced a massive decrease and this correlated with an abundance of C4 plants associated with reduced diversity. The shift of vegetation during this period was likely a result of a centennial severe drought period at ca. 950 cal years BP, as recorded in the literature and confirmed by the peak in aerophilous taxa in our diatom record. The drought was followed by a dramatic increase of fire occurrence and herbivory activities in the region, as recorded in the charcoal and spore records from both sites, indicating human activities at ca. 700 and 500 cal years BP for Lake Dangovavy and Tampoketsa-Ankazobe wetland, respectively. Though the vegetation at both sites in Central Highlands of Madagascar was very dynamic until ca. 1000 cal years BP, complex interactions between climate and fire allowed the forest and ericoid elements to persist, consistent with a heterogeneous mosaic landscape. This changed from 1000 years ago with the occurrence of a regional severe drought event followed by an increase in human activities leading to an increase of grass, a decline in forest and ericoid elements. Our findings suggest that although, the eastern and western slopes in Madagascar might have different vegetation histories over time as a response to the complex climatic-fire drivers at least until ca. 1000 cal years BP, they both: a) Contained ancient open ecosystems such as grasslands and/or ericoid shrubland, and a mosaic landscape which should be considered typical of the highland region. b) Experienced a loss of forest, woodland and mosaic elements, a trend that is consistent with the anthropogenic conversion of some forests to grasslands since ca. 1000 cal years BP. Such findings have implications in terms of conservation, fire management and afforestation projects in the Central Highlands, and provide additional knowledge that contributes to the understanding of its ecological processes and history prior to human arrival on the island. Indeed: 1) Ancient grasslands and ericoid shrubland need to be identified and conserved because of their antiquity and unique biodiversity. To date, there has been some focus on ancient grasslands, but the presence of ancient heathlands has not been discussed. 2) It is important to distinguish ancient from derived grasslands and to target the latter for reforestation, using species that are typical of the remaining forest patches. 3) Fire management should be conducted at a local scale and should incorporate the landscape fire history, considering, for example, the differences between two slopes in the Central Highlands.

The seasonal changes in freezing resistance and water relations in four dwarf shrub species of Ericaceae family: Vaccinium vitis-idaea, V. myrtillus, V. uliginosum and Oxycoccus palustris in two study areas differing in altitude were studied in this work. To establish the freezing resistance, the plants were sampled eight times, to determine parameters of the water relations, the plants were sampled six times during the growing season of 2009. For the freezing resistance examination, ice nucleation temperature (exotherm) and 50 per cent lethal temperature (LT50) were found. The water relations were described using the parameters derived from the pressure-volume curves: osmotic potential at full turgor, osmotic potential at zero turgor, cytoplasmic water fraction, relative water content at turgor loss and bulk modulus of elasticity. An important seasonal variability in the freezing resistance was found. The highest levels of the freezing resistance were reached in the spring and in the autumn, the lowest levels were found in the summer. There were also changes in the used mechanisms of the freezing resistance - for most of the year, the plants were tolerant, they showed the avoidance mechanism only in the summer. The seasonal changes in the water relation parameter were less unambiguous. The most of...

Le bleuet sauvage (Vaccinium angustifolium Ait. et V. myrtilloides Michaux) représente un marché en plein essor au Canada, premier pays producteur et exportateur mondial de ce fruit. Pour faire face à la demande, les producteurs cherchent continuellement à adapter leurs pratiques de production dans le but d’améliorer leur rendement et l'état de santé de leurs bleuetiers. Or, les micro-organismes présents dans les racines et dans le sol jouent un rôle non négligeable en lien avec la santé des plantes. Ce microbiote est donc d’intérêt d’un point de vue agronomique, pourtant, contrairement à d’autres cultures, très peu d’études se sont penchées spécifiquement sur le microbiote du milieu racinaire du bleuetier sauvage. Ce doctorat s’inscrit donc dans l’optique d’accroître les connaissances sur les communautés bactériennes et fongiques présentes dans les bleuetières au Québec. Les objectifs de ce projet sont de détecter les taxons qui pourraient avoir un impact sur les variables agronomiques des bleuetiers telles que le rendement; d’identifier les variables physico-chimiques du sol influençant ces communautés; et d’étudier les impacts que peuvent avoir les différentes pratiques agricoles, telles que la fertilisation et la fauche thermique, sur ces micro-organismes. Nous nous sommes appuyés sur le séquençage de nouvelle génération et le métacodage à barres de l’ADN environnemental de nos échantillons de racines et de sol afin d’obtenir une analyse des communautés bactériennes et fongiques de la rhizosphère et des racines des bleuetiers. Les analyses multivariées effectuées par la suite permettent de comparer ces communautés et de voir si certaines espèces sont spécifiques à une condition particulière. Dans l’ensemble, cette thèse a donc permis de caractériser les communautés fongiques et bactériennes du milieu racinaire du bleuetier sauvage in situ dans plusieurs bleuetières du Québec. De nombreuses espèces de champignons mycorhiziens éricoïdes ont été systématiquement identifiées dans les trois études et leur prédominance suggère leur importance pour le bleuetier sauvage. Nous avons également trouvé que l’ordre bactérien des Rhizobiales, connu pour sa capacité à fixer l’azote atmosphérique, occupait une part importante de la communauté bactérienne. Les études sur la fertilisation et la fauche thermique ont démontré que ces deux pratiques agricoles avaient peu d’impact significatif sur les communautés microbiennes étudiées. Enfin, cette thèse donne des pistes de réflexion sur la fixation d’azote par les communautés bactériennes et pose les premières bases pour des essais de bio-inoculation avec les espèces fongiques et bactériennes détectées ayant un potentiel impact bénéfique sur la culture des bleuets sauvages. / The wild blueberry (Vaccinium angustifolium Ait. and V. myrtilloides Michaux) market is booming in Canada, the world's leading producer and exporter of this fruit. In order to meet the demand, growers are constantly trying to adapt their production practices to improve their yields and the health of their blueberry fields. Micro-organisms present in the roots and in the soil play a significant role in the health of the plants. This microbiota is therefore of interest from an agronomic point of view, yet, contrary to other crops, very few studies have been conducted specifically on the microbiota of the root environment of wild blueberries. This doctoral project therefore aims at increasing our knowledge of the bacterial and fungal communities present in wild blueberry fields in Quebec. The objectives of this project are to detect taxa that could have an impact on agronomic variables of wild blueberry fields such as fruit yield; to identify soil physico-chemical variables influencing these communities; and to study the impacts that different agricultural practices, such as fertilization or thermal pruning, may have on these micro-organisms. We relied on next generation sequencing and metabarcoding of environmental DNA from our root and soil samples to obtain an analysis of the bacterial and fungal communities in the rhizosphere and roots of blueberry shrubs. Subsequent multivariate analyses allow us to compare these communities and see if certain species are specific to a particular condition. Overall, this thesis has characterized the fungal and bacterial communities in the root environment of wild blueberry in situ in several Quebec wild blueberry fields. Numerous species of ericoid mycorrhizal fungi were systematically identified in all three studies, and their predominance suggests their importance to wild blueberries. We also found that the bacterial order Rhizobiales, known for its ability to fix atmospheric nitrogen, occupied an important part of the bacterial community. Studies on fertilization and thermal mowing showed that these two agricultural practices have limited significant impacts on the microbial communities studied. Finally, this thesis provides insights into nitrogen fixation by bacterial communities and lays the groundwork for bio-inoculation trials with the fungal and bacterial species detected to have a potential beneficial impact on wild blueberry cultivation.

Il a été établi que la majorité des plantes vasculaires abritent des micro-organismes endophytes bactériens et fongiques, qui peuvent coloniser les tissus végétaux et former des associations allant du mutualisme à la pathogénèse. Les symbioses végétales mutualistes les plus communes impliquent les champignons endo-mycorhiziens arbusculaires (AMF). Ces champignons s’associent aux racines des plantes et leur permettent d’améliorer leur nutrition minérale, tandis qu’ils bénéficient des composés produits par l'hôte. Toutefois, les plantes de la famille Ericaceae s’engagent plutôt dans des associations mutualistes avec les champignons mycorhiziens éricoïdes (ErMF). Ces derniers sont morphologiquement et taxonomiquement mal définis, en apparence distribués aléatoirement parmi les espèces issues des grandes divisions taxonomiques des Ascomycota et Basidiomycota. En raison de cette incohérence taxonomique et de l'absence d'une histoire évolutive explicative, la diversité réelle de ces champignons est mal caractérisée. De ce fait, ce projet vise à étudier le microbiote associé à la plante Ericaceae Vaccinium macrocarpon Aït (canneberge), axant la recherche sur les angles morphologiques, génomiques et transcriptomiques des champignons de type ErMF et autres endophytes capables de contrôler la croissance des agents phytopathogènes et de stimuler la croissance des plantes. Notre première démarche présentée dans le chapitre 2 s’est focalisée sur la caractérisation du microbiote endophyte bactérien et fongique de la canneberge, une plante vivace principalement produite en Amérique du Nord, notamment au Québec. Nous avons isolé et identifié 180 micro-organismes à partir de plantes de cultivars variés, collectées de champs différents, et avons démontré l'existence d'une variabilité dans le microbiote selon les tissus, les cultivars, et même entre les champs d'une même ferme. Parmi les endophytes d’intérêt identifiés, l’isolat fongique Lachnum sp. EC5 a stimulé la croissance des cultivars de canneberge Stevens et Mullica Queen et a formé des structures intracellulaires similaires à celles des ErMF à l’intérieur des cellules racinaires de la canneberge. De plus, l’isolat EB37 identifié Bacillus velezensis s’est révélé être un puissant agent antifongique, montrant cependant une tolérance particulière au champignon Lachnum sp. EC5, lors des tests de confrontation. Ce volet sera détaillé avec plus de précision dans le chapitre 4. Le chapitre 3 a porté sur l’analyse génomique comparative de l’isolat fongique Lachnum sp. EC5 avec plusieurs espèces de champignons Leotiomycetes ErMF, saprophytes et pathogènes. Nous avons analysé le sécrétome protéique prédit de ces champignons et mis en évidence que les gènes codant pour les enzymes de dégradation des parois végétales ne sont pas corrélés au mode de vie fongique (mycorhizien, pathogène ou saprophyte). A l’inverse, 10 protéines effectrices de Lachnum sp. EC5 prédites pour cibler spécifiquement un compartiment intracellulaire chez les cellules végétales ont des similarités avec celles d’espèces mutualistes comme Meliniomyces variabilis et Oidiodendron maius. Aussi, la protéine effectrice putative Zn-MP, prédite pour cibler, potentiellement, les chloroplastes végétaux nous permet de proposer un rôle dans le renforcement de l’immunité végétale. Le chapitre 4 s’est intéressé aux mécanismes de régulation d'expression de gènes induits lors de l’interaction entre le champignon Lachnum sp. EC5 et la bactérie B. velezensis EB37. Ces mécanismes ont été comparés à ceux activés chez la bactérie en présence de champignons pathogènes. Nous avons démontré une physiologique cellulaire bactérienne distincte en présence de Lachnum sp. EC5, dénotée par une faible expression des gènes induits lors du stress nutritif associé aux processus de sporulation, de formation du biofilm, de secretion de CAZymes et de lipopeptides. Nous avons suggéré que la sous-régulation de ces mécanismes serait essentiellement explicable par une disponibilité plus importante en glucose ou en d’autres sources de carbone préférentielles pour la bactérie. En réponse, le champignon Lachnum sp. EC5 a vécu différents changements morphologiques. Il aurait détoxifié ses environnements intra et extra-cellulaires et surexprimé sa voie de production de carbone dépendante du cycle du glyoxylate, générant ainsi des conditions favorisant un contact physique entre les deux micro-organismes. En conclusion, nous avons argumenté et documenté que la définition des ErMF basée uniquement sur des critères morphologiques est mal adaptée à catégoriser ces champignons. Notre approche multidisciplinaire a mis en évidence la diversité du microbiote de la canneberge, a étendu la notion d’ErMF à d'autres champignons jusqu'ici exclus de ce groupe, et a souligné l'importance des associations interspécifiques sur l’interaction ErMF-plantes. Ces avancées permettront d’améliorer nos connaissances sur le microbiote des plantes éricacées contribuant, au développement de solutions environnementales éco-responsables pour l’industrie de la canneberge. / It has been established that the majority of vascular plants harbour bacterial and fungal endophytes that colonize plant tissues, and thus form associations that range from mutualism to pathogenesis. Mycorrhizal fungi are a particular class of endophytes that associate with plant roots and enhance plant mineral uptake. The most common type of mutualistic plant symbiosis involves arbuscular mycorrhizal fungi (AMF), whereas plants of the Ericaceae family instead engage in mutualistic associations with ericoid mycorrhizal fungi (ErMF). The ErMF group, in its current definition, includes both ascomycete and basidiomycete species, yet is morphologically, taxonomically and evolutionarily poorly defined, which implies that the group’s true diversity is not well understood. The objective of this project is to complement morphological information with genomic and transcriptomic data to better understand the role of ErMF in 1) controlling the negative effects of pathogenic infections, and 2) the potential plant growth stimulation for the Ericaceous plant Vaccinium macrocarpon Ait. Our first approach presented in Chapter 2 focused on the characterization of the bacterial and fungal endo-symbiotic microbiota of the Ericaceous plant, Vaccinium macrocarpon Ait (cranberry), a perennial plant mainly in North America, particularly in Quebec. We isolated ~180 distinct bacterial and fungal endophytes collected from roots, stems, and leaves of cranberry plants cultivated in Quebec, Canada. We show that the cranberry microbiome varies substantially between tissues, cultivars, and across fields of the same farm. Among the isolated endophytes, the fungus Lachnum sp. EC5 was found to promote the growth of cranberry cultivars Stevens and Mullica Queen, and to form intracellular structures resembling those other ErMF inside the cortical root cells. In addition, the bacterium Bacillus velezensis (EB37) has been found to be a potent antifungal agent. Interestingly, a confrontation test between EB37 and the fungus Lachnum sp. EC5 revealed a mutual tolerance, which we will describe later in chapter 4. In chapter 3, our project focused on the comparative genomic analysis of the fungus Lachnum sp. EC5 with several Leotiomycete ErMF, saprophytes and pathogens. We analyzed fungal secretomes and demonstrated that genes encoding plant cell wall degradation enzymes are conserved between the tested fungi which suggests that such proteins are not indicative of a particular fungal lifestyle. On the other hand, 10 effector proteins identified in Lachnum sp. EC5 were also only found in mutualistic fungi, such as Meliniomyces variabilis, Oidiodendron maius and have been reported to target the plant intracellular compartments. Also, the identification of the putative effector protein Zn-MP, specific to Lachnum sp. EC5 and predicted to target plant chloroplasts, suggest a role in the reinforcement of plant immunity. Chapter 4 focuses on the patterns of gene expression regulation induced in the biocontrol bacterium B. velezensis EB37 in interaction with the potentially mutualistic fungus Lachnum sp. EC5. These mechanisms were then compared to those activated when the bacterium is in the presence of pathogenic/saprophytic fungi. We demonstrated that in co-culture with Lachnum sp. EC5, EB37expresses fewer genes related to stress, and fewer related to the stationary phase which often involves production of bacterial biofilms and lipopeptides, such as mycosubtilin. We suggest that the lessened response to stress is related to an increased availability of glucose or other preferential sources of carbons for the bacterium. Conversely, Lachnum sp. EC5 in the presence of EB37 underwent morphological changes by a higher lateral branching., detoxified its external and internal environment by expressing both a catalase activity and efflux pumps, and overexpressed its glyoxylate cycle-dependent carbon production pathway, and thus promoting favourable conditions for close physical contact with the bacterium. In conclusion, we demonstrated that the morphological-based definitions are poorly adapted to the categorization of ErMF fungi. Our multidisciplinary approach highlighted the diversity of the cranberry microbiota, extended the notion of ErMF to other fungi hitherto excluded from this fungal group and underlined the importance of interspecific associations on the ErMF-plant interaction. These advances enhance our understanding of the Ericaceous plant microbiota and contributes to the development of sustainable solutions for the cranberry industry.